Diversity of <i>Phytophthora</i> Species Detected in Disturbed and Undisturbed British Soils Using High-Throughput Sequencing Targeting ITS rRNA and COI mtDNA Regions

• Main Authors: Blanca B. Landa, Luis F. Arias-Giraldo, Béatrice Henricot, Miguel Montes-Borrego, Lucas A. Shuttleworth, Ana Pérez-Sierra
• Format: Article
• Language: English
• Published: MDPI AG 2021-02-01
• Series: Forests
• Subjects: metabarcoding; forest diseases; oomycetes; soilborne pathogens
• Online Access: https://www.mdpi.com/1999-4907/12/2/229

Disease outbreaks caused by introduced <i>Phytophthora</i> species have been increasing in British forests and woodlands in recent years. A better knowledge of the <i>Phytophthora</i> communities already present in the UK is of great importance when developing management and mitigation strategies for these diseases. To do this, soils were sampled in “disturbed” sites, meaning sites frequently visited by the public, with recent and new plantings or soil disturbances versus more “natural” forest and woodland sites with little disturbance or management. <i>Phytophthora</i> diversity was assessed using high-throughput Illumina sequencing targeting the widely accepted barcoding Internal Transcribed Spacer 1 (ITS1) region of rRNA and comparing it with the mitochondrial cytochrome c oxidase I (COI) gene. Isolation of <i>Phytophthora</i> was run in parallel. <i>Nothophytophthora </i>spp. and <i>Phytophthora</i> spp. were detected in 79 and 41 of the 132 locations of the 14 studied sites when using ITS or COI, respectively. A total of 20 <i>Phytophthora</i> amplicon sequence variants (ASVs) were assigned to known <i>Phytophthora</i> species from eight clades (1a, 2, 2b, 3a, 5, 6b, 7a, 8b, 8c, 8d, 10a, and 10b) and 12 ASVs from six clades (1a, 2c, 3a, 3b, 6b, 7a, 8b, 8c, and 8d) when using ITS or COI, respectively. Only at two locations were the results in agreement for ITS, COI, and isolation. Additionally, 21 and 17 unknown <i>Phytophthora</i> phylotypes were detected using the ITS and COI, respectively. Several <i>Phytophthora</i> spp. within clades 7 and 8, including very important forest pathogens such as <i>P. austrocedri</i> and <i>P. ramorum</i>, were identified and found more frequently at “disturbed” sites. Additionally, eight ASVs identified as <i>Nothophytophthora</i> spp. were detected representing the first report of species within this new genus in Britain. Only three species not known to be present in Britain (<i>P. castaneae</i>, <i>P. capsici</i>, and <i>P. fallax</i>) were detected with the ITS primers and not with COI. To confirm the presence of these or any potential new <i>Phytophthora</i> species, sites should be re-sampled for confirmation. Additionally, there is a need to confirm if these species are a threat to British trees and try to establish any eradication measures required to mitigate <i>Phytophthora</i> spread in Britain.